Modified spectral count index (mSCI) for estimation of protein abundance by protein relative identification possibility (RIPpro): A new proteomic technological parameter

Journal of Proteome Research

Volumn 8, Issue 11, 2009, Pages 4934-4942

  Sun, Aihua ^a,b   Zhang, Jiyang ^b   Wang, Chunping ^a   Yang, Dong ^b   Wei, Handong ^b   Zhu, Yunping ^b   Jiang, Ying ^b   He, Fuchu ^a,b,c  

^a INSTITUTE OF BASIC MEDICAL SCIENCES   (China)

^b BEIJING INSTITUTE OF RADIATION MEDICINE   (China)

^c FUDAN UNIVERSITY   (China)

Author keywords

Correlation; Liver; Mass; Proteome; Quantification; Spectra; Transcriptome

Indexed keywords

MESSENGER RNA; PROTEIN;

ANIMAL CELL; ARTICLE; HUMAN; HUMAN TISSUE; LIVER; MOUSE; NONHUMAN; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEOMICS;

ALGORITHMS; ANIMALS; CELL LINE; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; HUMANS; MICE; PEPTIDES; PROTEINS; PROTEOMICS; REGRESSION ANALYSIS; REPRODUCIBILITY OF RESULTS; RNA, MESSENGER; SOFTWARE;

EID: 70449398034     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr900252n     Document Type: Article

References (45)

1. Corbin, R. W.; Paliy, O.; Yang, F.; Shabanowitz, J.; Platt, M.; Lyons, C. E., Jr.; Root, K.; McAuliffe, J.; Jordan, M. I.; Kustu, S.; Soupene, E.; Hunt, D. F. Toward a protein profile of Escherichia coli: comparison to its transcription profile. Proc. Natl. Acad. Sci. U.S.A. 2003, 100 (16), 9232-9237 (Pubitemid 37033912)
2. Ishihama, Y.; Oda, Y.; Tabata, T.; Sato, T.; Nagasu, T.; Rappsilber, J.; Mann, M. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol. Cell. Proteomics 2005, 4 (9), 1265-1272 (Pubitemid 41448714)
3. Old, W. M.; Meyer-Arendt, K.; Aveline-Wolf, L.; Pierce, K. G.; Mendoza, A.; Sevinsky, J. R.; Resing, K. A.; Ahn, N. G. Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol. Cell. Proteomics 2005, 4 (10), 1487-1502
4. Liu, H.; Sadygov, R. G.; Yates, J. R., III. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 2004, 76 (14), 4193-4201
5. Rappsilber, J.; Ryder, U.; Lamond, A. I.; Mann, M. Large-scale proteomic analysis of the human spliceosome. Genome Res. 2002, 12 (8), 1231-1245 (Pubitemid 41264425)
6. Nie, L.; Wu, G.; Zhang, W. Correlation of mRNA expression and protein abundance affected by multiple sequence features related to translational efficiency in Desulfovibrio vulgaris: a quantitative analysis. Genetics 2006, 174 (4), 2229-2243 (Pubitemid 46011608)
7. Heller, M.; Schlappritzi, E.; Stalder, D.; Nuoffer, J. M.; Haeberli, A. Compositional protein analysis of high density lipoproteins in hypercholesterolemia by shotgun LC-MS/MS and probabilistic peptide scoring. Mol. Cell. Proteomics 2007, 6 (6), 1059-1072 (Pubitemid 47019407)
8. Chan, E. Integrating Transcriptomics and Proteomics. Genomics Proteomics 2006, 6 (3.), 20-26.
9. Griffin, T. J.; Gygi, S. P.; Ideker, T.; Rist, B.; Eng, J.; Hood, L.; Aebersold, R. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol. Cell. Proteomics 2002, 1 (4), 323-333
10. Schmidt, M. W.; Houseman, A.; Ivanov, A. R.; Wolf, D. A. Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe. Mol. Syst. Biol. 2007, 3, 79.
11. Anderson, L.; Seilhamer, J. A comparison of selected mRNA and protein abundances in human liver. Electrophoresis 1997, 18 (3-4), 533-537 (Pubitemid 27174443)
12. Kislinger, T.; Cox, B.; Kannan, A.; Chung, C.; Hu, P.; Ignatchenko, A.; Scott, M. S.; Gramolini, A. O.; Morris, Q.; Hallett, M. T.; Rossant, J.; Hughes, T. R.; Frey, B.; Emili, A. Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell 2006, 125 (1), 173-186
13. Forner, F.; Foster, L. J.; Campanaro, S.; Valle, G.; Mann, M. Quantitative proteomic comparison of rat mitochondria from muscle, heart, and liver. Mol. Cell. Proteomics 2006, 5 (4), 608-619
14. Chen, G.; Gharib, T. G.; Huang, C. C.; Taylor, J. M.; Misek, D. E.; Kardia, S. L.; Giordano, T. J.; Iannettoni, M. D.; Orringer, M. B.; Hanash, S. M.; Beer, D. G. Discordant protein and mRNA expression in lung adenocarcinomas. Mol. Cell. Proteomics 2002, 1 (4), 304-313
15. Mootha, V. K.; Bunkenborg, J.; Olsen, J. V.; Hjerrild, M.; Wisniewski, J. R.; Stahl, E.; Bolouri, M. S.; Ray, H. N.; Sihag, S.; Kamal, M.; Patterson, N.; Lander, E. S.; Mann, M. Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell 2003, 115 (5), 629-640 (Pubitemid 37508523)
16. Washburn, M. P.; Koller, A.; Oshiro, G.; Ulaszek, R. R.; Plouffe, D.; Deciu, C.; Winzeler, E.; Yates, J. R., III. Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 2003, 100 (6), 3107-3112
17. Williamson, A. J.; Smith, D. L.; Blinco, D.; Unwin, R. D.; Pearson, S.; Wilson, C.; Miller, C.; Lancashire, L.; Lacaud, G.; Kouskoff, V.; Whetton, A. D. Quantitative proteomics analysis demonstrates post-transcriptional regulation of embryonic stem cell differentiation to hematopoiesis. Mol. Cell. Proteomics 2008, 7 (3), 459-472
18. Minagawa, H.; Honda, M.; Miyazaki, K.; Tabuse, Y.; Teramoto, R.; Yamashita, T.; Nishino, R.; Takatori, H.; Ueda, T.; Kamijo, K.; Kaneko, S. Comparative proteomic and transcriptomic profiling of the human hepatocellular carcinoma. Biochem. Biophys. Res. Commun. 2008, 366 (1), 186-192 (Pubitemid 350297227)
19. Irmler, M.; Hartl, D.; Schmidt, T.; Schuchhardt, J.; Lach, C.; Meyer, H. E.; Hrabe de Angelis, M.; Klose, J.; Beckers, J. An approach to handling and interpretation of ambiguous data in transcriptome and proteome comparisons. Proteomics 2008, 8 (6), 1165-1169
20. Ghaemmaghami, S.; Huh, W. K.; Bower, K.; Howson, R. W.; Belle, A.; Dephoure, N.; O'Shea, E. K.; Weissman, J. S. Global analysis of protein expression in yeast. Nature 2003, 425 (6959), 737-741 (Pubitemid 37314318)
21. Nie, L.; Wu, G.; Zhang, W. Correlation between mRNA and protein abundance in Desulfovibrio vulgaris: a multiple regression to identify sources of variations. Biochem. Biophys. Res. Commun. 2006, 339 (2), 603-610 (Pubitemid 41739710)
22. Cox, B.; Kislinger, T.; Emili, A. Integrating gene and protein expression data: pattern analysis and profile mining. Methods 2005, 35 (3), 303-314 (Pubitemid 40255595)
23. Hegde, P. S.; White, I. R.; Debouck, C. Interplay of transcriptomics and proteomics. Curr. Opin. Biotechnol. 2003, 14 (6), 647-651
24. Nie, L.; Wu, G.; Brockman, F. J.; Zhang, W. Integrated analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: zero-inflated Poisson regression models to predict abundance of undetected proteins. Bioinformatics 2006, 22 (13), 1641-1647 (Pubitemid 43985298)
25. Gygi, S. P.; Rochon, Y.; Franza, B. R.; Aebersold, R. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 1999, 19 (3), 1720-1730 (Pubitemid 29098230)
26. Nie, L.; Wu, G.; Culley, D. E.; Scholten, J. C.; Zhang, W. Integrative analysis of transcriptomic and proteomic data: challenges, solutions and applications. Crit. Rev. Biotechnol. 2007, 27 (2), 63-75. (Pubitemid 46956894)
27. Zheng, J.; Gao, X.; Mato, J.; Beretta, L.; He, F. Report of the 9th HLPP Workshop October 2007, Seoul, Korea. Proteomics 2008, 8 (17), 3420-3423
28. Hu 1.0, a publicly-available database. J. Proteome Res. 2009, DOI: 10.1021/pr900532r.
29. Xue XF, W. S.; Zu, Y. P.; He, F. C. Improving label-free protein quantification methods using expectation maximization-like algorithm in shotgun proteomics. Chin. J. Anal. Chem. 2007, 1, 19-24.
30. Zhang, W.; Morris, Q. D.; Chang, R.; Shai, O.; Bakowski, M. A.; Mitsakakis, N.; Mohammad, N.; Robinson, M. D.; Zirngibl, R.; Somogyi, E.; Laurin, N.; Eftekharpour, E.; Sat, E.; Grigull, J.; Pan, Q.; Peng, W. T.; Krogan, N.; Greenblatt, J.; Fehlings, M.; van der Kooy, D.; Aubin, J.; Bruneau, B. G.; Rossant, J.; Blencowe, B. J.; Frey, B. J.; Hughes, T. R. The functional landscape of mouse gene expression. J. Biol. 2004, 3 (5), 21.
31. Su, A. I.; Wiltshire, T.; Batalov, S.; Lapp, H.; Ching, K. A.; Block, D.; Zhang, J.; Soden, R.; Hayakawa, M.; Kreiman, G.; Cooke, M. P.; Walker, J. R.; Hogenesch, J. B. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. U.S.A. 2004, 101 (16), 6062-6067 (Pubitemid 38520528)
32. Wilkins, M. R.; Gasteiger, E.; Bairoch, A.; Sanchez, J. C.; Williams, K. L.; Appel, R. D.; Hochstrasser, D. F. Protein identification and analysis tools in the ExPASy server. Methods Mol. Biol. 1999, 112, 531-552
33. Li, D.; Li, J. Q.; Ouyang, S. G.; S.F., W.; Wang, J.; Xu, X. J.; Zhu, Y. P.; He, F. C. An Integrated Strategy for Functional Analysis in Large-scale Proteomic Research by Gene Ontology. Prog. Biochem. Biophys. 2005, 32 (11), 1026-1029
34. Ideker, T.; Thorsson, V.; Ranish, J. A.; Christmas, R.; Buhler, J.; Eng, J. K.; Bumgarner, R.; Goodlett, D. R.; Aebersold, R.; Hood, L. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 2001, 292 (5518), 929-934 (Pubitemid 32422490)
35. Eisen, M. B.; Spellman, P. T.; Brown, P. O.; Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. U.S.A. 1998, 95 (25), 14863-14868 (Pubitemid 29003722)
36. Shen, Y.; Zhao, R.; Berger, S. J.; Anderson, G. A.; Rodriguez, N.; Smith, R. D. High-efficiency nanoscale liquid chromatography coupled on-line with mass spectrometry using nanoelectrospray ionization for proteomics. Anal. Chem. 2002, 74 (16), 4235-4249
37. Wu, G.; Nie, L.; Zhang, W. Relation between mRNA expression and sequence information in Desulfovibrio vulgaris: combinatorial contributions of upstream regulatory motifs and coding sequence features to variations in mRNA abundance. Biochem. Biophys. Res. Commun. 2006, 344 (1), 114-121
38. Moore, D. S.; McCabe, G. P. Introduction to the Practice of Statistics; W.H. Freeman: New York, 1999.
39. Lian, Z.; Kluger, Y.; Greenbaum, D. S.; Tuck, D.; Gerstein, M.; Berliner, N.; Weissman, S. M.; Newburger, P. E. Genomic and proteomic analysis of the myeloid differentiation program: global analysis of gene expression during induced differentiation in the MPRO cell line. Blood 2002, 100 (9), 3209-3220
40. Chen, G.; Gharib, T. G.; Wang, H.; Huang, C. C.; Kuick, R.; Thomas, D. G.; Shedden, K. A.; Misek, D. E.; Taylor, J. M.; Giordano, T. J.; Kardia, S. L.; Iannettoni, M. D.; Yee, J.; Hogg, P. J.; Orringer, M. B.; Hanash, S. M.; Beer, D. G. Protein profiles associated with survival in lung adenocarcinoma. Proc. Natl. Acad. Sci. U.S.A. 2003, 100 (23), 13537-13542 (Pubitemid 37444777)
41. Coghlan, A.; Wolfe, K. H. Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast 2000, 16 (12), 1131-1145
42. Urrutia, A. O.; Hurst, L. D. The signature of selection mediated by expression on human genes. Genome Res. 2003, 13 (10), 2260-2264 (Pubitemid 37265991)
43. Lemos, B.; Bettencourt, B. R.; Meiklejohn, C. D.; Hartl, D. L. Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions. Mol. Biol. Evol. 2005, 22 (5), 1345-1354
44. Warringer, J.; Blomberg, A. Evolutionary constraints on yeast protein size. BMC Evol. Biol. 2006, 6, 61. (Pubitemid 44367165)
45. Belle, A.; Tanay, A.; Bitincka, L.; Shamir, R.; O'Shea, E. K. Quantification of protein half-lives in the budding yeast proteome. Proc. Natl. Acad. Sci. U.S.A. 2006, 103 (35), 13004-13009 (Pubitemid 44338907)